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This is a tutorial to guide the analysis of RNAseq datasets using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL.

For details instructions to setup the transcriptutorial (data, software, R packages, etc), visit

This tutorial is split into several sections, from normalisation to causal network analysis. Once set up, you may run each step sequentially. The corresponding R markdown scripts for each of those sections can be found in the scripts subfolder.

  1. Normalisation

  2. Differential analysis

  3. Pathway activity with Progeny

  4. Trascription factors activity with Dorothea/Viper

  5. Network reconstruction with CARNIVAL

  6. Analysis of CARNIVAL results

For any question/suggestions, we encourage you to use the issue submission system :)

Have fun!